.get_data_by_sample | R Documentation |
Internal Function to Get Mutations/CNA/Fusion By Sample ID
.get_data_by_sample(
sample_id = NULL,
study_id = NULL,
molecular_profile_id = NULL,
sample_study_pairs = NULL,
data_type = c("mutation", "cna", "fusion", "structural_variant", "segment"),
genes = NULL,
panel = NULL,
add_hugo = TRUE,
base_url = NULL
)
sample_id |
a vector of sample IDs (character) |
study_id |
A string indicating the study ID from which to pull data. If no study ID, will
guess the study ID based on your URL and inform. Only 1 study ID can be passed. If mutations/cna from
more than 1 study needed, see |
molecular_profile_id |
A string indicating the molecular profile ID from which to pull data. If ID supplied, will
guess the molecular profile ID based on the study ID. Only 1 molecular profile ID can be passed. If mutations from
more than 1 study needed, see |
sample_study_pairs |
A dataframe with columns: |
data_type |
specify what type of data to return. Options are |
genes |
A vector of Entrez ids or Hugo symbols. If Hugo symbols are supplied, they will be converted to entrez ids using the |
panel |
One or more panel IDs to query (e.g. 'IMPACT468').
If |
add_hugo |
Logical indicating whether |
base_url |
The database URL to query
If |
A dataframe of mutations, CNAs or fusions.
## Not run:
set_cbioportal_db("public")
.get_data_by_sample(sample_id = c("TCGA-OR-A5J2-01","TCGA-OR-A5J6-01"),
study_id = "acc_tcga", data_type = "mutation")
.get_data_by_sample(sample_id = c("DS-sig-010-P2"),
molecular_profile_id = "blca_plasmacytoid_mskcc_2016_cna", data_type = "cna")
.get_data_by_sample(sample_id = c("P-0002146-T01-IM3"),
study_id = "blca_plasmacytoid_mskcc_2016", data_type = "fusion")
df_pairs <- data.frame(
"sample_id" = c("s_C_36924L_P001_d",
"s_C_03LNU8_P001_d"),
"study_id" = c("prad_msk_2019"))
.get_data_by_sample(sample_study_pairs = df_pairs, data_type = "mutation")
.get_data_by_sample(sample_study_pairs = df_pairs, genes = 7157, data_type = "mutation")
.get_data_by_sample(sample_study_pairs = df_pairs, data_type = "cna")
.get_data_by_sample(sample_study_pairs = df_pairs, data_type = "fusion")
df_pairs2 <- data.frame(
"sample_id" = c("P-0002146-T01-IM3", "s_C_CAUWT7_P001_d"),
"study_id" = c("blca_plasmacytoid_mskcc_2016", "prad_msk_2019"))
.get_data_by_sample(sample_study_pairs = df_pairs2, data_type = "mutation")
.get_data_by_sample(sample_study_pairs = df_pairs2, genes = 7157)
.get_data_by_sample(sample_study_pairs = df_pairs2, data_type = "cna")
.get_data_by_sample(sample_study_pairs = df_pairs2, data_type = "fusion")
## End(Not run)
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